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Sample GSM4658334 Query DataSets for GSM4658334
Status Public on Oct 22, 2020
Title SF8628_DMSO_2
Sample type SRA
 
Source name diffuse intrinsic pontine glioma
Organism Homo sapiens
Characteristics cell line: SF8628
passage: 10-15
agent: DMSO
Treatment protocol The small-molecule inhibitor used in this study is PTC-028 (orb181369, Biorbyt). This drug was dissolved in DMSO to make stock concentrations to use in in vitro experiments.Stable knockdown of genes was carried out using shRNAs targeting different genes. Briefly, the cells (~100,000/well) were seeded onto a 6-well plate and the cells were transduced with the lentiviral shRNA using polybrene (polybrene final concentration of 8 ng/ml). Transduced cells were selected using puromycin (2µg/ml) and the cells were routinely maintained in the cell culture medium containing 1µg/ml of puromycin. ShRNAs targeting BMI1 was obtained from transOMIC technologies and from the Functional Genomic Core Facility at the University of Colorado, Denver.
Growth protocol DMEM-High glucose (Invitrogen), 10% fetal bovine serum (Atlanta Biologicals), 1% Non-Essential Amino Acids, 1% Antibiotic-Antimycotic
Extracted molecule total RNA
Extraction protocol RNA from cell lines were extracted with a RNeasy Plus RNA kit (Qiagen) and the purity of the RNA isolated was examined using an Agilent 2100 bioanalyzer.
mRNA libraries were made from the isolated pure RNA and RNA sequencing was performed using Nova-Seq.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description SF8628_PTC028_raw_counts.txt
Data processing The reads were trimmed and clipped for quality control in Trimmomatic (v0.36).
Read quality was checked for each sample using FastQC v0.10.1.
High quality reads were then imported into STAR (v2.4.0.1) for alignment into BAM files.
The function summarizeOverlaps from the GenomicAlignments package (v1.16.0) was used to count the reads from BAM files.
DESeq (v1.32.0) was then used to get differential expression genes on the raw counts.
Alignment was done using the transcriptome hg38 (from UCSC)
Genome_build: hg38
Supplementary_files_format_and_content: txt file includes raw read counts.
 
Submission date Jul 07, 2020
Last update date Oct 22, 2020
Contact name Etienne Danis
E-mail(s) etienne.danis@cuanschutz.edu
Organization name University of Colorado, Denver - Anschutz Medical Campus
Street address 12800 E. 19th Ave
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
 
Platform ID GPL24676
Series (1)
GSE140768 Senescence induced by BMI1 inhibition is a therapeutic vulnerability in H3K27M-mutant DIPG
Relations
BioSample SAMN15462223
SRA SRX8677622

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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